diff --git a/DESCRIPTION b/DESCRIPTION index 080dbdd5f..3c30d0df5 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.1.0.9021 +Version: 1.2.0 Date: 2020-05-28 Title: Antimicrobial Resistance Analysis Authors@R: c( diff --git a/NAMESPACE b/NAMESPACE index 2249a670b..43f56b966 100755 --- a/NAMESPACE +++ b/NAMESPACE @@ -195,61 +195,6 @@ export(set_mo_source) export(skewness) export(susceptibility) export(theme_rsi) -exportMethods("[.ab") -exportMethods("[.disk") -exportMethods("[.mic") -exportMethods("[.mo") -exportMethods("[<-.ab") -exportMethods("[<-.disk") -exportMethods("[<-.mic") -exportMethods("[<-.mo") -exportMethods("[<-.rsi") -exportMethods("[[.ab") -exportMethods("[[.disk") -exportMethods("[[.mic") -exportMethods("[[.mo") -exportMethods("[[<-.ab") -exportMethods("[[<-.disk") -exportMethods("[[<-.mic") -exportMethods("[[<-.mo") -exportMethods("[[<-.rsi") -exportMethods(as.data.frame.ab) -exportMethods(as.data.frame.mo) -exportMethods(as.double.mic) -exportMethods(as.integer.mic) -exportMethods(as.numeric.mic) -exportMethods(barplot.mic) -exportMethods(barplot.rsi) -exportMethods(c.ab) -exportMethods(c.disk) -exportMethods(c.mic) -exportMethods(c.mo) -exportMethods(c.rsi) -exportMethods(droplevels.mic) -exportMethods(droplevels.rsi) -exportMethods(format.bug_drug_combinations) -exportMethods(kurtosis) -exportMethods(kurtosis.data.frame) -exportMethods(kurtosis.default) -exportMethods(kurtosis.matrix) -exportMethods(plot.mic) -exportMethods(plot.rsi) -exportMethods(print.ab) -exportMethods(print.bug_drug_combinations) -exportMethods(print.catalogue_of_life_version) -exportMethods(print.disk) -exportMethods(print.mic) -exportMethods(print.mo) -exportMethods(print.mo_renamed) -exportMethods(print.mo_uncertainties) -exportMethods(print.rsi) -exportMethods(skewness) -exportMethods(skewness.data.frame) -exportMethods(skewness.default) -exportMethods(skewness.matrix) -exportMethods(summary.mic) -exportMethods(summary.mo) -exportMethods(summary.rsi) importFrom(graphics,arrows) importFrom(graphics,axis) importFrom(graphics,barplot) diff --git a/NEWS.md b/NEWS.md index adcd3e51b..ebf649cc4 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,5 @@ -# AMR 1.1.0.9021 -## Last updated: 28-May-2020 +# AMR 1.2.0 + ### Breaking * Removed code dependency on all other R packages, making this package fully independent of the development process of others. This is a major code change, but will probably not be noticeable by most users. diff --git a/R/ab.R b/R/ab.R index ebdbab098..6c7ca3ebc 100755 --- a/R/ab.R +++ b/R/ab.R @@ -343,7 +343,7 @@ is.ab <- function(x) { inherits(x, "ab") } -#' @exportMethod print.ab +#' @method print ab #' @export #' @noRd print.ab <- function(x, ...) { @@ -351,7 +351,7 @@ print.ab <- function(x, ...) { print(as.character(x), quote = FALSE) } -#' @exportMethod as.data.frame.ab +#' @method as.data.frame ab #' @export #' @noRd as.data.frame.ab <- function(x, ...) { @@ -362,7 +362,7 @@ as.data.frame.ab <- function(x, ...) { as.data.frame.vector(as.ab(x), ...) } } -#' @exportMethod [.ab +#' @method [ ab #' @export #' @noRd "[.ab" <- function(x, ...) { @@ -370,7 +370,7 @@ as.data.frame.ab <- function(x, ...) { attributes(y) <- attributes(x) y } -#' @exportMethod [[.ab +#' @method [[ ab #' @export #' @noRd "[[.ab" <- function(x, ...) { @@ -378,7 +378,7 @@ as.data.frame.ab <- function(x, ...) { attributes(y) <- attributes(x) y } -#' @exportMethod [<-.ab +#' @method [<- ab #' @export #' @noRd "[<-.ab" <- function(i, j, ..., value) { @@ -386,7 +386,7 @@ as.data.frame.ab <- function(x, ...) { attributes(y) <- attributes(i) class_integrity_check(y, "antimicrobial code", antibiotics$ab) } -#' @exportMethod [[<-.ab +#' @method [[<- ab #' @export #' @noRd "[[<-.ab" <- function(i, j, ..., value) { @@ -394,7 +394,7 @@ as.data.frame.ab <- function(x, ...) { attributes(y) <- attributes(i) class_integrity_check(y, "antimicrobial code", antibiotics$ab) } -#' @exportMethod c.ab +#' @method c ab #' @export #' @noRd c.ab <- function(x, ...) { diff --git a/R/bug_drug_combinations.R b/R/bug_drug_combinations.R index 3e2405d98..da731829b 100644 --- a/R/bug_drug_combinations.R +++ b/R/bug_drug_combinations.R @@ -107,7 +107,7 @@ bug_drug_combinations <- function(x, structure(.Data = out, class = c("bug_drug_combinations", class(x))) } -#' @exportMethod format.bug_drug_combinations +#' @method format bug_drug_combinations #' @export #' @rdname bug_drug_combinations format.bug_drug_combinations <- function(x, @@ -218,7 +218,7 @@ format.bug_drug_combinations <- function(x, y } -#' @exportMethod print.bug_drug_combinations +#' @method print bug_drug_combinations #' @export print.bug_drug_combinations <- function(x, ...) { print(as.data.frame(x, stringsAsFactors = FALSE)) diff --git a/R/catalogue_of_life.R b/R/catalogue_of_life.R index d89387666..9fc0b5bbf 100755 --- a/R/catalogue_of_life.R +++ b/R/catalogue_of_life.R @@ -107,7 +107,7 @@ catalogue_of_life_version <- function() { class = c("catalogue_of_life_version", "list")) } -#' @exportMethod print.catalogue_of_life_version +#' @method print catalogue_of_life_version #' @export #' @noRd print.catalogue_of_life_version <- function(x, ...) { diff --git a/R/disk.R b/R/disk.R index 96ac06f1f..b8b403cb2 100644 --- a/R/disk.R +++ b/R/disk.R @@ -95,7 +95,7 @@ is.disk <- function(x) { inherits(x, "disk") } -#' @exportMethod print.disk +#' @method print disk #' @export #' @noRd print.disk <- function(x, ...) { @@ -103,7 +103,7 @@ print.disk <- function(x, ...) { print(as.integer(x), quote = FALSE) } -#' @exportMethod [.disk +#' @method [ disk #' @export #' @noRd "[.disk" <- function(x, ...) { @@ -111,7 +111,7 @@ print.disk <- function(x, ...) { attributes(y) <- attributes(x) y } -#' @exportMethod [[.disk +#' @method [[ disk #' @export #' @noRd "[[.disk" <- function(x, ...) { @@ -119,7 +119,7 @@ print.disk <- function(x, ...) { attributes(y) <- attributes(x) y } -#' @exportMethod [<-.disk +#' @method [<- disk #' @export #' @noRd "[<-.disk" <- function(i, j, ..., value) { @@ -128,7 +128,7 @@ print.disk <- function(x, ...) { attributes(y) <- attributes(i) y } -#' @exportMethod [[<-.disk +#' @method [[<- disk #' @export #' @noRd "[[<-.disk" <- function(i, j, ..., value) { @@ -137,7 +137,7 @@ print.disk <- function(x, ...) { attributes(y) <- attributes(i) y } -#' @exportMethod c.disk +#' @method c disk #' @export #' @noRd c.disk <- function(x, ...) { diff --git a/R/kurtosis.R b/R/kurtosis.R index f2b019c92..40c2c16da 100755 --- a/R/kurtosis.R +++ b/R/kurtosis.R @@ -25,7 +25,6 @@ #' @inheritSection lifecycle Questioning lifecycle #' @param x a vector of values, a [`matrix`] or a [`data.frame`] #' @param na.rm a logical value indicating whether `NA` values should be stripped before the computation proceeds. -#' @exportMethod kurtosis #' @seealso [skewness()] #' @rdname kurtosis #' @inheritSection AMR Read more on our website! @@ -34,7 +33,7 @@ kurtosis <- function(x, na.rm = FALSE) { UseMethod("kurtosis") } -#' @exportMethod kurtosis.default +#' @method kurtosis default #' @rdname kurtosis #' @export kurtosis.default <- function(x, na.rm = FALSE) { @@ -47,14 +46,14 @@ kurtosis.default <- function(x, na.rm = FALSE) { (base::sum((x - base::mean(x, na.rm = na.rm))^2, na.rm = na.rm)^2) } -#' @exportMethod kurtosis.matrix +#' @method kurtosis matrix #' @rdname kurtosis #' @export kurtosis.matrix <- function(x, na.rm = FALSE) { base::apply(x, 2, kurtosis.default, na.rm = na.rm) } -#' @exportMethod kurtosis.data.frame +#' @method kurtosis data.frame #' @rdname kurtosis #' @export kurtosis.data.frame <- function(x, na.rm = FALSE) { diff --git a/R/mic.R b/R/mic.R index 8f7cdb03b..1715b87d8 100755 --- a/R/mic.R +++ b/R/mic.R @@ -140,28 +140,28 @@ is.mic <- function(x) { inherits(x, "mic") } -#' @exportMethod as.double.mic +#' @method as.double mic #' @export #' @noRd as.double.mic <- function(x, ...) { as.double(gsub("(<|=|>)+", "", as.character(x))) } -#' @exportMethod as.integer.mic +#' @method as.integer mic #' @export #' @noRd as.integer.mic <- function(x, ...) { as.integer(gsub("(<|=|>)+", "", as.character(x))) } -#' @exportMethod as.numeric.mic +#' @method as.numeric mic #' @export #' @noRd as.numeric.mic <- function(x, ...) { as.numeric(gsub("(<|=|>)+", "", as.character(x))) } -#' @exportMethod droplevels.mic +#' @method droplevels mic #' @export #' @noRd droplevels.mic <- function(x, exclude = ifelse(anyNA(levels(x)), NULL, NA), ...) { @@ -170,7 +170,7 @@ droplevels.mic <- function(x, exclude = ifelse(anyNA(levels(x)), NULL, NA), ...) x } -#' @exportMethod print.mic +#' @method print mic #' @export #' @noRd print.mic <- function(x, ...) { @@ -178,7 +178,7 @@ print.mic <- function(x, ...) { print(as.character(x), quote = FALSE) } -#' @exportMethod summary.mic +#' @method summary mic #' @export #' @noRd summary.mic <- function(object, ...) { @@ -194,7 +194,7 @@ summary.mic <- function(object, ...) { ) } -#' @exportMethod plot.mic +#' @method plot mic #' @export #' @importFrom graphics barplot axis par #' @noRd @@ -213,7 +213,7 @@ plot.mic <- function(x, axis(2, seq(0, max(table(droplevels.factor(x))))) } -#' @exportMethod barplot.mic +#' @method barplot mic #' @export #' @importFrom graphics barplot axis #' @noRd @@ -232,7 +232,7 @@ barplot.mic <- function(height, axis(2, seq(0, max(table(droplevels.factor(height))))) } -#' @exportMethod [.mic +#' @method [ mic #' @export #' @noRd "[.mic" <- function(x, ...) { @@ -240,7 +240,7 @@ barplot.mic <- function(height, attributes(y) <- attributes(x) y } -#' @exportMethod [[.mic +#' @method [[ mic #' @export #' @noRd "[[.mic" <- function(x, ...) { @@ -248,7 +248,7 @@ barplot.mic <- function(height, attributes(y) <- attributes(x) y } -#' @exportMethod [<-.mic +#' @method [<- mic #' @export #' @noRd "[<-.mic" <- function(i, j, ..., value) { @@ -257,7 +257,7 @@ barplot.mic <- function(height, attributes(y) <- attributes(i) y } -#' @exportMethod [[<-.mic +#' @method [[<- mic #' @export #' @noRd "[[<-.mic" <- function(i, j, ..., value) { @@ -266,7 +266,7 @@ barplot.mic <- function(height, attributes(y) <- attributes(i) y } -#' @exportMethod c.mic +#' @method c mic #' @export #' @noRd c.mic <- function(x, ...) { diff --git a/R/mo.R b/R/mo.R index 9d2270ad7..fc6594bfe 100755 --- a/R/mo.R +++ b/R/mo.R @@ -1566,7 +1566,7 @@ format_uncertainty_as_df <- function(uncertainty_level, df } -#' @exportMethod print.mo +#' @method print mo #' @export #' @noRd print.mo <- function(x, ...) { @@ -1577,7 +1577,7 @@ print.mo <- function(x, ...) { print.default(x, quote = FALSE) } -#' @exportMethod summary.mo +#' @method summary mo #' @export #' @noRd summary.mo <- function(object, ...) { @@ -1593,7 +1593,7 @@ summary.mo <- function(object, ...) { "#3" = top_3[3]) } -#' @exportMethod as.data.frame.mo +#' @method as.data.frame mo #' @export #' @noRd as.data.frame.mo <- function(x, ...) { @@ -1605,7 +1605,7 @@ as.data.frame.mo <- function(x, ...) { } } -#' @exportMethod [.mo +#' @method [ mo #' @export #' @noRd "[.mo" <- function(x, ...) { @@ -1613,7 +1613,7 @@ as.data.frame.mo <- function(x, ...) { attributes(y) <- attributes(x) y } -#' @exportMethod [[.mo +#' @method [[ mo #' @export #' @noRd "[[.mo" <- function(x, ...) { @@ -1621,7 +1621,7 @@ as.data.frame.mo <- function(x, ...) { attributes(y) <- attributes(x) y } -#' @exportMethod [<-.mo +#' @method [<- mo #' @export #' @noRd "[<-.mo" <- function(i, j, ..., value) { @@ -1631,7 +1631,7 @@ as.data.frame.mo <- function(x, ...) { class_integrity_check(y, "microorganism code", c(as.character(microorganisms$mo), as.character(microorganisms.translation$mo_old))) } -#' @exportMethod [[<-.mo +#' @method [[<- mo #' @export #' @noRd "[[<-.mo" <- function(i, j, ..., value) { @@ -1641,7 +1641,7 @@ as.data.frame.mo <- function(x, ...) { class_integrity_check(y, "microorganism code", c(as.character(microorganisms$mo), as.character(microorganisms.translation$mo_old))) } -#' @exportMethod c.mo +#' @method c mo #' @export #' @noRd c.mo <- function(x, ...) { @@ -1668,7 +1668,7 @@ mo_uncertainties <- function() { class = c("mo_uncertainties", "data.frame")) } -#' @exportMethod print.mo_uncertainties +#' @method print mo_uncertainties #' @export #' @noRd print.mo_uncertainties <- function(x, ...) { @@ -1717,7 +1717,7 @@ mo_renamed <- function() { class = c("mo_renamed", "data.frame")) } -#' @exportMethod print.mo_renamed +#' @method print mo_renamed #' @export #' @noRd print.mo_renamed <- function(x, ...) { diff --git a/R/resistance_predict.R b/R/resistance_predict.R index 5d77df5a2..d121836a7 100755 --- a/R/resistance_predict.R +++ b/R/resistance_predict.R @@ -302,7 +302,7 @@ resistance_predict <- function(x, #' @export rsi_predict <- resistance_predict -#' @exportMethod plot.mic +#' @method plot resistance_predict #' @export #' @importFrom graphics axis arrows points #' @rdname resistance_predict diff --git a/R/rsi.R b/R/rsi.R index 9d16b432c..35cd711a9 100755 --- a/R/rsi.R +++ b/R/rsi.R @@ -529,7 +529,7 @@ is.rsi.eligible <- function(x, threshold = 0.05) { } } -#' @exportMethod print.rsi +#' @method print rsi #' @export #' @noRd print.rsi <- function(x, ...) { @@ -537,7 +537,7 @@ print.rsi <- function(x, ...) { print(as.character(x), quote = FALSE) } -#' @exportMethod droplevels.rsi +#' @method droplevels rsi #' @export #' @noRd droplevels.rsi <- function(x, exclude = if (anyNA(levels(x))) NULL else NA, ...) { @@ -546,7 +546,7 @@ droplevels.rsi <- function(x, exclude = if (anyNA(levels(x))) NULL else NA, ...) x } -#' @exportMethod summary.rsi +#' @method summary rsi #' @export #' @noRd summary.rsi <- function(object, ...) { @@ -561,7 +561,7 @@ summary.rsi <- function(object, ...) { ) } -#' @exportMethod plot.rsi +#' @method plot rsi #' @export #' @importFrom graphics text axis #' @noRd @@ -618,7 +618,7 @@ plot.rsi <- function(x, } -#' @exportMethod barplot.rsi +#' @method barplot rsi #' @export #' @importFrom graphics barplot axis par #' @noRd @@ -652,7 +652,7 @@ barplot.rsi <- function(height, } } -#' @exportMethod [<-.rsi +#' @method [<- rsi #' @export #' @noRd "[<-.rsi" <- function(i, j, ..., value) { @@ -661,7 +661,7 @@ barplot.rsi <- function(height, attributes(y) <- attributes(i) y } -#' @exportMethod [[<-.rsi +#' @method [[<- rsi #' @export #' @noRd "[[<-.rsi" <- function(i, j, ..., value) { @@ -670,7 +670,7 @@ barplot.rsi <- function(height, attributes(y) <- attributes(i) y } -#' @exportMethod c.rsi +#' @method c rsi #' @export #' @noRd c.rsi <- function(x, ...) { diff --git a/R/skewness.R b/R/skewness.R index 35d2458f7..455de80cd 100755 --- a/R/skewness.R +++ b/R/skewness.R @@ -27,7 +27,6 @@ #' @inheritSection lifecycle Questioning lifecycle #' @param x a vector of values, a [`matrix`] or a [`data.frame`] #' @param na.rm a logical value indicating whether `NA` values should be stripped before the computation proceeds. -#' @exportMethod skewness #' @seealso [kurtosis()] #' @rdname skewness #' @inheritSection AMR Read more on our website! @@ -36,7 +35,7 @@ skewness <- function(x, na.rm = FALSE) { UseMethod("skewness") } -#' @exportMethod skewness.default +#' @method skewness default #' @rdname skewness #' @export skewness.default <- function(x, na.rm = FALSE) { @@ -48,14 +47,14 @@ skewness.default <- function(x, na.rm = FALSE) { (base::sum((x - base::mean(x))^3) / n) / (base::sum((x - base::mean(x)) ^ 2) / n) ^ (3 / 2) } -#' @exportMethod skewness.matrix +#' @method skewness matrix #' @rdname skewness #' @export skewness.matrix <- function(x, na.rm = FALSE) { base::apply(x, 2, skewness.default, na.rm = na.rm) } -#' @exportMethod skewness.data.frame +#' @method skewness data.frame #' @rdname skewness #' @export skewness.data.frame <- function(x, na.rm = FALSE) { diff --git a/cran-comments.md b/cran-comments.md index d5de3b057..5652aa725 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,5 +1,3 @@ -* Although the previous release (1.0.1) is from 2020-02-23, this updates provides support for the upcoming dplyr 1.0.0 which is used (and relied upon) by probably all our users. - -* For this specific version, otherwise nothing to mention. +* For this specific version, nothing to mention. * Since version 0.3.0, CHECK returns a NOTE for having a data directory over 3 MB. This is needed to offer users reference data for the complete taxonomy of microorganisms - one of the most important features of this package. diff --git a/docs/404.html b/docs/404.html index 40d22457f..528cd0c44 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,7 +81,7 @@ AMR (for R) - 1.1.0.9021 + 1.2.0 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 070e9fa7a..351386e67 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ AMR (for R) - 1.1.0.9021 + 1.2.0 diff --git a/docs/articles/AMR.html b/docs/articles/AMR.html index fd671271c..7fbe24258 100644 --- a/docs/articles/AMR.html +++ b/docs/articles/AMR.html @@ -39,7 +39,7 @@ AMR (for R) - 1.1.0.9021 + 1.2.0 @@ -336,54 +336,32 @@ -2015-07-23 -Z5 -Hospital B -Streptococcus pneumoniae -S -S -S -S -F - - -2017-01-21 -D6 -Hospital C -Staphylococcus aureus -S -S -S -S -M - - -2014-05-20 -Y10 +2013-12-18 +P10 Hospital A Escherichia coli +R S -I S S F -2017-11-02 -M10 -Hospital D -Staphylococcus aureus +2010-07-10 +K6 +Hospital C +Escherichia coli +S S S -R S M -2014-08-26 -B4 +2014-12-14 +F6 Hospital C -Staphylococcus aureus +Escherichia coli S S S @@ -391,11 +369,33 @@ M -2013-05-29 -R3 +2010-12-31 +N8 +Hospital D +Escherichia coli +S +S +S +S +F + + +2010-11-24 +M5 Hospital B Escherichia coli S +S +S +S +M + + +2010-10-07 +Z8 +Hospital C +Escherichia coli +R R S S @@ -432,16 +432,16 @@ Longest: 1

1 M -10,518 -52.59% -10,518 -52.59% +10,397 +51.99% +10,397 +51.99% 2 F -9,482 -47.41% +9,603 +48.02% 20,000 100.00% @@ -491,7 +491,7 @@ Longest: 1

First weighted isolates

-

We made a slight twist to the CLSI algorithm, to take into account the antimicrobial susceptibility profile. Have a look at all isolates of patient P10, sorted on date:

+

We made a slight twist to the CLSI algorithm, to take into account the antimicrobial susceptibility profile. Have a look at all isolates of patient U2, sorted on date:

@@ -507,10 +507,10 @@ Longest: 1

- - + + - + @@ -518,43 +518,43 @@ Longest: 1

- - + + - - - + + + - - + + + + - - - - + + - - + + - - + + - + @@ -562,62 +562,62 @@ Longest: 1

- - + + + - - - + + - + - - + + + - - + - - + + + - - + - - + + - +
isolate
12010-01-22P102010-03-30U2 B_ESCHR_COLIIR S S S
22010-02-24P102010-07-30U2 B_ESCHR_COLISSS RSSS FALSE
32010-03-10P102010-10-14U2 B_ESCHR_COLIRS S SRR FALSE
42010-03-25P102010-12-17U2 B_ESCHR_COLIR S SRSS FALSE
52010-04-30P102011-02-17U2 B_ESCHR_COLISR S S S
62010-05-05P102011-03-17U2 B_ESCHR_COLII S SR S FALSE
72010-05-19P102011-06-10U2 B_ESCHR_COLI R S S SFALSETRUE
82010-05-27P102011-07-17U2 B_ESCHR_COLIR S SSSR FALSE
92010-10-01P102011-08-08U2 B_ESCHR_COLII SSSR S FALSE
102010-11-19P102011-08-21U2 B_ESCHR_COLI SR SR S FALSE
-

Only 1 isolates are marked as ‘first’ according to CLSI guideline. But when reviewing the antibiogram, it is obvious that some isolates are absolutely different strains and should be included too. This is why we weigh isolates, based on their antibiogram. The key_antibiotics() function adds a vector with 18 key antibiotics: 6 broad spectrum ones, 6 small spectrum for Gram negatives and 6 small spectrum for Gram positives. These can be defined by the user.

+

Only 2 isolates are marked as ‘first’ according to CLSI guideline. But when reviewing the antibiogram, it is obvious that some isolates are absolutely different strains and should be included too. This is why we weigh isolates, based on their antibiogram. The key_antibiotics() function adds a vector with 18 key antibiotics: 6 broad spectrum ones, 6 small spectrum for Gram negatives and 6 small spectrum for Gram positives. These can be defined by the user.

If a column exists with a name like ‘key(…)ab’ the first_isolate() function will automatically use it and determine the first weighted isolates. Mind the NOTEs in below output:

data <- data %>%
   mutate(keyab = key_antibiotics(.)) %>%
@@ -643,10 +643,10 @@ Longest: 1

 
 
 1
-2010-01-22
-P10
+2010-03-30
+U2
 B_ESCHR_COLI
-I
+R
 S
 S
 S
@@ -655,46 +655,46 @@ Longest: 1

 
 
 2
-2010-02-24
-P10
+2010-07-30
+U2
 B_ESCHR_COLI
-S
-S
-S
 R
+S
+S
+S
+FALSE
 FALSE
-TRUE
 
 
 3
-2010-03-10
-P10
+2010-10-14
+U2
 B_ESCHR_COLI
+R
+S
 S
 S
-R
-R
 FALSE
-TRUE
+FALSE
 
 
 4
-2010-03-25
-P10
+2010-12-17
+U2
 B_ESCHR_COLI
-R
 S
 S
-R
+S
+S
 FALSE
 TRUE
 
 
 5
-2010-04-30
-P10
+2011-02-17
+U2
 B_ESCHR_COLI
-S
+R
 S
 S
 S
@@ -703,71 +703,71 @@ Longest: 1

 
 
 6
-2010-05-05
-P10
+2011-03-17
+U2
 B_ESCHR_COLI
+I
 S
 S
-R
 S
 FALSE
-TRUE
+FALSE
 
 
 7
-2010-05-19
-P10
+2011-06-10
+U2
 B_ESCHR_COLI
 R
 S
 S
 S
-FALSE
+TRUE
 TRUE
 
 
 8
-2010-05-27
-P10
+2011-07-17
+U2
 B_ESCHR_COLI
+R
 S
 S
-S
-S
+R
 FALSE
 TRUE
 
 
 9
-2010-10-01
-P10
-B_ESCHR_COLI
-S
-S
-S
-S
-FALSE
-FALSE
-
-
-10
-2010-11-19
-P10
+2011-08-08
+U2
 B_ESCHR_COLI
+I
 S
 R
 S
-S
 FALSE
 TRUE
 
+
+10
+2011-08-21
+U2
+B_ESCHR_COLI
+S
+S
+R
+S
+FALSE
+FALSE
+
 
 
-
Instead of 1, now 9 isolates are flagged. In total, 78.3% of all isolates are marked ‘first weighted’ - 49.8% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.

+
Instead of 2, now 6 isolates are flagged. In total, 78.7% of all isolates are marked ‘first weighted’ - 50.2% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.

 
As with filter_first_isolate(), there’s a shortcut for this new algorithm too:

 
data_1st <- data %>%
   filter_first_weighted_isolate()

-
So we end up with 15,654 isolates for analysis.

+
So we end up with 15,741 isolates for analysis.

 
We can remove unneeded columns:

 
data_1st <- data_1st %>%
   select(-c(first, keyab))

@@ -775,7 +775,6 @@ Longest: 1

 
head(data_1st)

 
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data_1st %>% freq(genus, species)
Frequency table
Class: character

-Length: 15,654

-Available: 15,654 (100%, NA: 0 = 0%)

+Length: 15,741

+Available: 15,741 (100%, NA: 0 = 0%)

 Unique: 4
Shortest: 16

 Longest: 24

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The functions resistance() and susceptibility() can be used to calculate antimicrobial resistance or susceptibility. For more specific analyses, the functions proportion_S(), proportion_SI(), proportion_I(), proportion_IR() and proportion_R() can be used to determine the proportion of a specific antimicrobial outcome.
As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (proportion_R(), equal to resistance()) and susceptibility as the proportion of S and I (proportion_SI(), equal to susceptibility()). These functions can be used on their own:
data_1st %>% resistance(AMX)
-# [1] 0.4435288

+# [1] 0.4476209
Or can be used in conjuction with group_by() and summarise(), both from the dplyr package:
data_1st %>%
   group_by(hospital) %>%
@@ -975,19 +968,19 @@ Longest: 24

 

-
+
-
+
-
+
-
+

 

 date
 patient_id
 hospital
 

 
 
12015-07-23Z5Hospital BB_STRPT_PNMNSSSRFGram-positiveStreptococcuspneumoniaeTRUE
22017-01-21D6Hospital CB_STPHY_AURSSSSSMGram-positiveStaphylococcusaureusTRUE
42017-11-02M10Hospital DB_STPHY_AURSSSRSMGram-positiveStaphylococcusaureusTRUE
52014-08-26B4Hospital CB_STPHY_AURSSSSSMGram-positiveStaphylococcusaureusTRUE
62013-05-29R3Hospital B2013-12-18P10Hospital A
 B_ESCHR_COLIS
 R
 S
 SS
 F
 Gram-negative
 Escherichia
 TRUE
 

 
72013-12-10T32010-07-10K6Hospital CB_ESCHR_COLISSSSMGram-negativeEscherichiacoliTRUE
2014-12-14F6Hospital CB_ESCHR_COLISSSSMGram-negativeEscherichiacoliTRUE
2010-12-31N8Hospital DB_ESCHR_COLISSSSFGram-negativeEscherichiacoliTRUE
2010-11-24M5
 Hospital B
 B_ESCHR_COLI
 S
 S
 S
 SMGram-negativeEscherichiacoliTRUE
2010-10-07Z8Hospital CB_ESCHR_COLIRRSS
 F
 Gram-negative
 Escherichia
 
 
 
 
 

 1
 Escherichia coli7,77849.69%7,77849.69%7,94350.46%7,94350.46%
 

 

 2
 Staphylococcus aureus3,99925.55%11,77775.23%3,97825.27%11,92175.73%
 

 

 3
 Streptococcus pneumoniae2,30014.69%14,07789.93%2,24814.28%14,16990.01%
 

 

 4
 Klebsiella pneumoniae1,57710.07%15,6541,5729.99%15,741
 100.00%
 

 
 
 
 
 
 
 

 Hospital A0.44612390.4402730
 

 

 Hospital B0.44047620.4607609
 

 

 Hospital C0.45497630.4437526
 

 

 Hospital D0.43666880.4389635
 

 
 

@@ -1005,23 +998,23 @@ Longest: 24

 
 
 Hospital A
-0.4461239
-4631
+0.4402730
+4688
 
 
 Hospital B
-0.4404762
-5544
+0.4607609
+5441
 
 
 Hospital C
-0.4549763
-2321
+0.4437526
+2409
 
 
 Hospital D
-0.4366688
-3158
+0.4389635
+3203
 
 
 
@@ -1041,27 +1034,27 @@ Longest: 24

 
 
 Escherichia
-0.8215480
-0.8976601
-0.9835433
+0.8296613
+0.8992824
+0.9862772
 
 
 Klebsiella
-0.8300571
-0.8972733
-0.9866836
+0.8250636
+0.9083969
+0.9840967
 
 
 Staphylococcus
-0.8202051
-0.9229807
-0.9832458
+0.8245349
+0.9263449
+0.9891905
 
 
 Streptococcus
-0.6204348
+0.6107651
 0.0000000
-0.6204348
+0.6107651
 
 
 
diff --git a/docs/articles/AMR_files/figure-html/plot 1-1.png b/docs/articles/AMR_files/figure-html/plot 1-1.png
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diff --git a/docs/articles/EUCAST.html b/docs/articles/EUCAST.html
index 4f787ab12..42fb770fd 100644
--- a/docs/articles/EUCAST.html
+++ b/docs/articles/EUCAST.html
@@ -39,7 +39,7 @@
       
       
         AMR (for R)
-        1.1.0.9016
+        1.2.0
@@ -186,7 +186,7 @@

How to apply EUCAST rules

Matthijs S. Berends

-

21 May 2020

+

28 May 2020

Source: vignettes/EUCAST.Rmd @@ -301,6 +301,8 @@ 
eucast_rules(data)
+
# Warning: Not all columns with antimicrobial results are of class <rsi>.
+# Transform eligible columns to class <rsi> on beforehand: your_data %>% mutate_if(is.rsi.eligible, as.rsi)
diff --git a/docs/articles/MDR.html b/docs/articles/MDR.html index cc06cb1fb..f5b31017a 100644 --- a/docs/articles/MDR.html +++ b/docs/articles/MDR.html @@ -39,7 +39,7 @@ AMR (for R) - 1.1.0.9021 + 1.2.0 @@ -302,19 +302,19 @@ Unique: 2

The data set now looks like this:

head(my_TB_data)
 #   rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin
-# 1          R         S            R          I            I            S
-# 2          S         R            S          I            R            I
-# 3          S         S            I          S            R            R
-# 4          I         R            S          S            I            S
-# 5          S         S            R          R            R            S
-# 6          I         R            R          R            R            S
+# 1          S         R            R          S            R            R
+# 2          R         S            R          S            R            S
+# 3          R         R            S          S            R            S
+# 4          S         S            S          S            R            S
+# 5          S         R            S          S            R            S
+# 6          R         S            R          S            S            S
 #   kanamycin
 # 1         R
-# 2         S
-# 3         I
+# 2         I
+# 3         R
 # 4         S
 # 5         R
-# 6         I
+# 6 S

We can now add the interpretation of MDR-TB to our data set. You can use:

mdro(my_TB_data, guideline = "TB")

or its shortcut mdr_tb():

@@ -343,40 +343,40 @@ Unique: 5

- - - - + + + + - - - - + + + + - - - - + + + + - - - - + + + + - - + + diff --git a/docs/articles/PCA.html b/docs/articles/PCA.html index e65fca7d8..6694bba81 100644 --- a/docs/articles/PCA.html +++ b/docs/articles/PCA.html @@ -39,7 +39,7 @@ AMR (for R) - 1.1.0.9021 + 1.2.0 diff --git a/docs/articles/SPSS.html b/docs/articles/SPSS.html index 87da5d0ca..11cde0ec6 100644 --- a/docs/articles/SPSS.html +++ b/docs/articles/SPSS.html @@ -39,7 +39,7 @@ AMR (for R) - 1.1.0 + 1.2.0 @@ -186,7 +186,7 @@

How to import data from SPSS / SAS / Stata

Matthijs S. Berends

-

15 April 2020

+

28 May 2020

Source: vignettes/SPSS.Rmd @@ -242,10 +242,10 @@

To demonstrate the first point:

# not all values are valid MIC values:
 as.mic(0.125)
-# Class 'mic'
+# Class <mic>
 # [1] 0.125
 as.mic("testvalue")
-# Class 'mic'
+# Class <mic>
 # [1] <NA>
 
 # the Gram stain is avaiable for all bacteria:
@@ -398,7 +398,7 @@
-

Site built with pkgdown 1.5.0.

+

Site built with pkgdown 1.5.1.

diff --git a/docs/articles/WHONET.html b/docs/articles/WHONET.html index ce6c2ad47..15652aaf2 100644 --- a/docs/articles/WHONET.html +++ b/docs/articles/WHONET.html @@ -39,7 +39,7 @@ AMR (for R) - 1.1.0.9015 + 1.2.0 @@ -186,7 +186,7 @@

How to work with WHONET data

Matthijs S. Berends

-

20 May 2020

+

28 May 2020

Source: vignettes/WHONET.Rmd @@ -232,7 +232,7 @@

Class: character
Length: 500
Available: 500 (100%, NA: 0 = 0%)
-Unique: 39

+Unique: 37

Shortest: 11
Longest: 40

mo
1 Mono-resistant319263.84%319263.84%324564.90%324564.90%
2 Negative66713.34%385977.18%67813.56%392378.46%
3 Multi-drug-resistant63712.74%449689.92%60712.14%453090.60%
4 Poly-resistant2875.74%478395.66%2625.24%479295.84%
5 Extensively drug-resistant2174.34%2084.16% 5000 100.00%
@@ -319,15 +319,15 @@ Longest: 40

- - - - - + + + + +
10Enterococcus columbae40.8%44388.6%Streptococcus anginosus51.0%44488.8%
-

(omitted 29 entries, n = 57 [11.40%])

+

(omitted 27 entries, n = 56 [11.20%])

# our transformed antibiotic columns
 # amoxicillin/clavulanic acid (J01CR02) as an example
 data %>% freq(AMC_ND2)
diff --git a/docs/articles/benchmarks.html b/docs/articles/benchmarks.html index 6485137be..e86204ede 100644 --- a/docs/articles/benchmarks.html +++ b/docs/articles/benchmarks.html @@ -39,7 +39,7 @@ AMR (for R) - 1.1.0.9021 + 1.2.0
@@ -221,21 +221,21 @@ times = 10) print(S.aureus, unit = "ms", signif = 2) # Unit: milliseconds -# expr min lq mean median uq max -# as.mo("sau") 8.2 9.7 22.0 14.0 38.0 43 -# as.mo("stau") 130.0 130.0 160.0 170.0 170.0 190 -# as.mo("STAU") 120.0 130.0 150.0 150.0 180.0 190 -# as.mo("staaur") 8.3 9.1 13.0 9.4 10.0 40 -# as.mo("STAAUR") 8.0 9.3 15.0 10.0 13.0 35 -# as.mo("S. aureus") 9.3 11.0 26.0 14.0 15.0 120 -# as.mo("S aureus") 10.0 12.0 22.0 13.0 38.0 49 -# as.mo("Staphylococcus aureus") 6.6 7.7 8.5 8.6 9.1 10 -# as.mo("Staphylococcus aureus (MRSA)") 820.0 860.0 890.0 880.0 930.0 1000 -# as.mo("Sthafilokkockus aaureuz") 350.0 350.0 370.0 370.0 370.0 380 -# as.mo("MRSA") 7.8 9.1 13.0 10.0 11.0 42 -# as.mo("VISA") 11.0 12.0 19.0 13.0 15.0 47 -# as.mo("VRSA") 11.0 12.0 21.0 14.0 39.0 42 -# as.mo(22242419) 130.0 140.0 150.0 140.0 150.0 190 +# expr min lq mean median uq max +# as.mo("sau") 8.5 11.0 17.0 12.0 12.0 43.0 +# as.mo("stau") 120.0 130.0 150.0 140.0 160.0 180.0 +# as.mo("STAU") 130.0 140.0 150.0 150.0 160.0 170.0 +# as.mo("staaur") 7.7 9.1 13.0 11.0 12.0 38.0 +# as.mo("STAAUR") 8.3 9.3 15.0 10.0 11.0 37.0 +# as.mo("S. aureus") 11.0 12.0 18.0 13.0 14.0 41.0 +# as.mo("S aureus") 8.8 11.0 17.0 12.0 13.0 41.0 +# as.mo("Staphylococcus aureus") 6.4 6.6 7.4 7.6 7.8 9.1 +# as.mo("Staphylococcus aureus (MRSA)") 810.0 870.0 890.0 890.0 900.0 1000.0 +# as.mo("Sthafilokkockus aaureuz") 320.0 340.0 370.0 350.0 400.0 490.0 +# as.mo("MRSA") 9.2 10.0 13.0 11.0 12.0 37.0 +# as.mo("VISA") 12.0 12.0 22.0 13.0 43.0 44.0 +# as.mo("VRSA") 11.0 13.0 21.0 14.0 38.0 41.0 +# as.mo(22242419) 130.0 140.0 150.0 140.0 170.0 200.0 # neval # 10 # 10 @@ -262,12 +262,12 @@ times = 10) print(M.semesiae, unit = "ms", signif = 4) # Unit: milliseconds -# expr min lq mean median uq max -# as.mo("metsem") 135.600 143.500 157.800 153.400 175.70 191.40 -# as.mo("METSEM") 139.700 140.800 158.100 148.300 176.10 188.50 -# as.mo("M. semesiae") 9.010 9.317 13.280 9.802 12.51 40.46 -# as.mo("M. semesiae") 9.155 9.321 9.665 9.557 10.07 10.37 -# as.mo("Methanosarcina semesiae") 6.737 7.160 16.020 8.413 33.21 37.10 +# expr min lq mean median uq max +# as.mo("metsem") 143.400 146.300 156.10 155.400 164.900 176.40 +# as.mo("METSEM") 141.600 146.900 167.00 170.700 185.000 188.00 +# as.mo("M. semesiae") 9.665 9.879 16.50 10.090 11.960 44.29 +# as.mo("M. semesiae") 10.000 10.080 14.46 11.660 13.140 42.01 +# as.mo("Methanosarcina semesiae") 7.161 7.389 10.40 7.542 9.294 33.00 # neval # 10 # 10 @@ -307,7 +307,7 @@ print(run_it, unit = "ms", signif = 3) # Unit: milliseconds # expr min lq mean median uq max neval -# mo_name(x) 1670 1740 1800 1790 1880 1900 10 +# mo_name(x) 1650 1730 1790 1790 1840 1900 10

So transforming 500,000 values (!!) of 50 unique values only takes 1.79 seconds. You only lose time on your unique input values.

@@ -320,10 +320,10 @@ times = 10) print(run_it, unit = "ms", signif = 3) # Unit: milliseconds -# expr min lq mean median uq max neval -# A 5.630 5.900 6.420 6.480 6.910 7.120 10 -# B 9.940 11.300 15.000 11.800 12.300 45.300 10 -# C 0.247 0.277 0.315 0.295 0.358 0.386 10
+# expr min lq mean median uq max neval +# A 5.680 5.820 9.61 6.36 6.850 39.500 10 +# B 9.790 10.000 10.60 10.40 10.900 11.900 10 +# C 0.229 0.259 0.27 0.27 0.286 0.311 10

So going from mo_name("Staphylococcus aureus") to "Staphylococcus aureus" takes 0.0003 seconds - it doesn’t even start calculating if the result would be the same as the expected resulting value. That goes for all helper functions:

run_it <- microbenchmark(A = mo_species("aureus"),
                          B = mo_genus("Staphylococcus"),
@@ -337,14 +337,14 @@
 print(run_it, unit = "ms", signif = 3)
 # Unit: milliseconds
 #  expr   min    lq  mean median    uq   max neval
-#     A 0.207 0.214 0.241  0.218 0.240 0.412    10
-#     B 0.178 0.207 0.215  0.211 0.219 0.272    10
-#     C 0.218 0.221 0.234  0.233 0.240 0.264    10
-#     D 0.203 0.211 0.221  0.214 0.218 0.290    10
-#     E 0.208 0.209 0.223  0.214 0.227 0.279    10
-#     F 0.172 0.203 0.222  0.212 0.222 0.302    10
-#     G 0.200 0.202 0.212  0.208 0.213 0.253    10
-#     H 0.193 0.194 0.208  0.200 0.215 0.261    10
+# A 0.209 0.221 0.236 0.225 0.244 0.311 10 +# B 0.197 0.201 0.215 0.212 0.222 0.266 10 +# C 0.205 0.224 0.243 0.229 0.242 0.383 10 +# D 0.199 0.207 0.216 0.211 0.214 0.270 10 +# E 0.196 0.206 0.218 0.215 0.221 0.270 10 +# F 0.188 0.197 0.212 0.210 0.216 0.269 10 +# G 0.195 0.198 0.213 0.203 0.215 0.299 10 +# H 0.184 0.193 0.205 0.201 0.207 0.252 10

Of course, when running mo_phylum("Firmicutes") the function has zero knowledge about the actual microorganism, namely S. aureus. But since the result would be "Firmicutes" anyway, there is no point in calculating the result. And because this package ‘knows’ all phyla of all known bacteria (according to the Catalogue of Life), it can just return the initial value immediately.

@@ -370,14 +370,14 @@ times = 100) print(run_it, unit = "ms", signif = 4) # Unit: milliseconds -# expr min lq mean median uq max neval -# en 11.24 11.97 16.09 13.31 13.71 48.40 100 -# de 12.18 12.84 19.63 14.33 15.00 55.14 100 -# nl 16.24 17.07 24.36 18.61 19.83 55.70 100 -# es 12.23 12.77 17.38 13.71 14.72 51.57 100 -# it 12.15 13.01 18.55 14.03 14.81 146.90 100 -# fr 12.23 13.08 16.81 14.30 14.86 49.30 100 -# pt 12.30 12.85 18.13 14.24 14.88 49.70 100
+# expr min lq mean median uq max neval +# en 9.303 11.59 14.90 12.40 13.63 45.92 100 +# de 10.080 12.39 15.77 13.11 14.45 46.27 100 +# nl 13.200 16.26 20.88 17.80 19.52 49.93 100 +# es 9.957 12.23 15.57 13.12 14.59 51.99 100 +# it 10.210 12.44 19.02 13.34 14.74 52.96 100 +# fr 10.040 12.40 18.90 13.26 15.07 54.40 100 +# pt 10.450 12.67 16.91 13.46 14.68 51.47 100

Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.

diff --git a/docs/articles/benchmarks_files/figure-html/unnamed-chunk-4-1.png b/docs/articles/benchmarks_files/figure-html/unnamed-chunk-4-1.png index 78c0b6101..c83b2d1bc 100644 Binary files a/docs/articles/benchmarks_files/figure-html/unnamed-chunk-4-1.png and b/docs/articles/benchmarks_files/figure-html/unnamed-chunk-4-1.png differ diff --git a/docs/articles/benchmarks_files/figure-html/unnamed-chunk-6-1.png b/docs/articles/benchmarks_files/figure-html/unnamed-chunk-6-1.png index c48d8145f..e5d3f4c9b 100644 Binary files a/docs/articles/benchmarks_files/figure-html/unnamed-chunk-6-1.png and b/docs/articles/benchmarks_files/figure-html/unnamed-chunk-6-1.png differ diff --git a/docs/articles/index.html b/docs/articles/index.html index 77f6f0c58..a46a31768 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.1.0.9021 + 1.2.0 diff --git a/docs/articles/resistance_predict.html b/docs/articles/resistance_predict.html index 234dd590e..e6db163aa 100644 --- a/docs/articles/resistance_predict.html +++ b/docs/articles/resistance_predict.html @@ -39,7 +39,7 @@ AMR (for R) - 1.1.0.9021 + 1.2.0 diff --git a/docs/authors.html b/docs/authors.html index 94e69a1fe..5e489fbd3 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,7 +81,7 @@ AMR (for R) - 1.1.0.9021 + 1.2.0 diff --git a/docs/index.html b/docs/index.html index 5070eb9ca..7758a0524 100644 --- a/docs/index.html +++ b/docs/index.html @@ -43,7 +43,7 @@ AMR (for R) - 1.1.0.9021 + 1.2.0 diff --git a/docs/news/index.html b/docs/news/index.html index 619e5378a..315a90ca9 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.1.0.9021 + 1.2.0 @@ -229,14 +229,10 @@ Source: NEWS.md -
-

-AMR 1.1.0.9021 Unreleased +
+

+AMR 1.2.0 Unreleased

-
-

-Last updated: 28-May-2020 -

Breaking

@@ -296,7 +292,6 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
  • Removed function read.4d(), that was only useful for reading data from an old test database.
    • -

    diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 0ea0b5508..d52695207 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -10,7 +10,7 @@ articles: WHONET: WHONET.html benchmarks: benchmarks.html resistance_predict: resistance_predict.html -last_built: 2020-05-28T08:48Z +last_built: 2020-05-28T10:26Z urls: reference: https://msberends.gitlab.io/AMR/reference article: https://msberends.gitlab.io/AMR/articles diff --git a/docs/reference/AMR-deprecated.html b/docs/reference/AMR-deprecated.html index 52cf1a2c3..81947548b 100644 --- a/docs/reference/AMR-deprecated.html +++ b/docs/reference/AMR-deprecated.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9019 + 1.2.0

    diff --git a/docs/reference/AMR.html b/docs/reference/AMR.html index dd7cb8a37..b666f314a 100644 --- a/docs/reference/AMR.html +++ b/docs/reference/AMR.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0 + 1.2.0

    @@ -293,7 +293,7 @@ The Netherlands

    -

    Site built with pkgdown 1.5.0.

    +

    Site built with pkgdown 1.5.1.

    diff --git a/docs/reference/WHOCC.html b/docs/reference/WHOCC.html index 2812292f3..2f397f2c1 100644 --- a/docs/reference/WHOCC.html +++ b/docs/reference/WHOCC.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0 + 1.2.0 @@ -272,7 +272,7 @@ This package contains all ~550 antibiotic, antimycotic and antiviral dru
    -

    Site built with pkgdown 1.5.0.

    +

    Site built with pkgdown 1.5.1.

    diff --git a/docs/reference/WHONET.html b/docs/reference/WHONET.html index 9ac0f8fd9..1c678316d 100644 --- a/docs/reference/WHONET.html +++ b/docs/reference/WHONET.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0 + 1.2.0 @@ -290,7 +290,7 @@
    -

    Site built with pkgdown 1.5.0.

    +

    Site built with pkgdown 1.5.1.

    diff --git a/docs/reference/ab_property.html b/docs/reference/ab_property.html index 2c263ed78..1d598718a 100644 --- a/docs/reference/ab_property.html +++ b/docs/reference/ab_property.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9021 + 1.2.0 diff --git a/docs/reference/age.html b/docs/reference/age.html index 77680ac6d..805ebac03 100644 --- a/docs/reference/age.html +++ b/docs/reference/age.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/age_groups.html b/docs/reference/age_groups.html index 9c7b920ad..b8efb20b5 100644 --- a/docs/reference/age_groups.html +++ b/docs/reference/age_groups.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/antibiotics.html b/docs/reference/antibiotics.html index 8e3f313c3..a4dd3a172 100644 --- a/docs/reference/antibiotics.html +++ b/docs/reference/antibiotics.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9004 + 1.2.0 diff --git a/docs/reference/as.ab.html b/docs/reference/as.ab.html index 4f7f03c73..566ceae5e 100644 --- a/docs/reference/as.ab.html +++ b/docs/reference/as.ab.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/as.disk.html b/docs/reference/as.disk.html index ee1d4777e..ce24cf291 100644 --- a/docs/reference/as.disk.html +++ b/docs/reference/as.disk.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9020 + 1.2.0 diff --git a/docs/reference/as.mic.html b/docs/reference/as.mic.html index a3f93b345..d89457ab0 100644 --- a/docs/reference/as.mic.html +++ b/docs/reference/as.mic.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9020 + 1.2.0 diff --git a/docs/reference/as.mo.html b/docs/reference/as.mo.html index 7e05b9d65..d845cce97 100644 --- a/docs/reference/as.mo.html +++ b/docs/reference/as.mo.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9021 + 1.2.0 diff --git a/docs/reference/as.rsi.html b/docs/reference/as.rsi.html index 5a004e201..7daad110a 100644 --- a/docs/reference/as.rsi.html +++ b/docs/reference/as.rsi.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9020 + 1.2.0 diff --git a/docs/reference/atc_online.html b/docs/reference/atc_online.html index 198a5f7b7..3d7fd6bba 100644 --- a/docs/reference/atc_online.html +++ b/docs/reference/atc_online.html @@ -83,7 +83,7 @@ This function requires an internet connection." /> AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/availability.html b/docs/reference/availability.html index ffbde8be7..b1ca9639b 100644 --- a/docs/reference/availability.html +++ b/docs/reference/availability.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/bug_drug_combinations.html b/docs/reference/bug_drug_combinations.html index d9f685181..fcd717542 100644 --- a/docs/reference/bug_drug_combinations.html +++ b/docs/reference/bug_drug_combinations.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/catalogue_of_life.html b/docs/reference/catalogue_of_life.html index 5b70de3bc..ed7cf2c52 100644 --- a/docs/reference/catalogue_of_life.html +++ b/docs/reference/catalogue_of_life.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9021 + 1.2.0 diff --git a/docs/reference/catalogue_of_life_version.html b/docs/reference/catalogue_of_life_version.html index 5c066aeed..836074f6c 100644 --- a/docs/reference/catalogue_of_life_version.html +++ b/docs/reference/catalogue_of_life_version.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9015 + 1.2.0 diff --git a/docs/reference/count.html b/docs/reference/count.html index c986cf798..c2ddf447e 100644 --- a/docs/reference/count.html +++ b/docs/reference/count.html @@ -83,7 +83,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible( AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/eucast_rules.html b/docs/reference/eucast_rules.html index a4fe41a37..66b33bf8f 100644 --- a/docs/reference/eucast_rules.html +++ b/docs/reference/eucast_rules.html @@ -83,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/example_isolates.html b/docs/reference/example_isolates.html index c5727c45e..19c332ce6 100644 --- a/docs/reference/example_isolates.html +++ b/docs/reference/example_isolates.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0 + 1.2.0 @@ -274,7 +274,7 @@
    -

    Site built with pkgdown 1.5.0.

    +

    Site built with pkgdown 1.5.1.

    diff --git a/docs/reference/example_isolates_unclean.html b/docs/reference/example_isolates_unclean.html index 2c482a405..9f84ea4fd 100644 --- a/docs/reference/example_isolates_unclean.html +++ b/docs/reference/example_isolates_unclean.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0 + 1.2.0 @@ -269,7 +269,7 @@
    -

    Site built with pkgdown 1.5.0.

    +

    Site built with pkgdown 1.5.1.

    diff --git a/docs/reference/filter_ab_class.html b/docs/reference/filter_ab_class.html index f94370003..192b0fbd0 100644 --- a/docs/reference/filter_ab_class.html +++ b/docs/reference/filter_ab_class.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/first_isolate.html b/docs/reference/first_isolate.html index 5989e3c96..2bf68dc24 100644 --- a/docs/reference/first_isolate.html +++ b/docs/reference/first_isolate.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/g.test.html b/docs/reference/g.test.html index 54a548871..bafe27042 100644 --- a/docs/reference/g.test.html +++ b/docs/reference/g.test.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/ggplot_pca.html b/docs/reference/ggplot_pca.html index 2dc3a8d20..2920f01a6 100644 --- a/docs/reference/ggplot_pca.html +++ b/docs/reference/ggplot_pca.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/ggplot_rsi.html b/docs/reference/ggplot_rsi.html index e90bc0cee..e060340dd 100644 --- a/docs/reference/ggplot_rsi.html +++ b/docs/reference/ggplot_rsi.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/guess_ab_col.html b/docs/reference/guess_ab_col.html index 9ed3ecd59..ea215ecd3 100644 --- a/docs/reference/guess_ab_col.html +++ b/docs/reference/guess_ab_col.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/index.html b/docs/reference/index.html index dba6713c1..2517794f2 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.1.0.9021 + 1.2.0 diff --git a/docs/reference/join.html b/docs/reference/join.html index fcc9912f4..f16555b5d 100644 --- a/docs/reference/join.html +++ b/docs/reference/join.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/key_antibiotics.html b/docs/reference/key_antibiotics.html index f528d6635..21ef75b39 100644 --- a/docs/reference/key_antibiotics.html +++ b/docs/reference/key_antibiotics.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/kurtosis.html b/docs/reference/kurtosis.html index da3c30fdf..c963c0601 100644 --- a/docs/reference/kurtosis.html +++ b/docs/reference/kurtosis.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/lifecycle.html b/docs/reference/lifecycle.html index 170248bc4..e0dd74327 100644 --- a/docs/reference/lifecycle.html +++ b/docs/reference/lifecycle.html @@ -84,7 +84,7 @@ This page contains a section for every lifecycle (with text borrowed from the af AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/like.html b/docs/reference/like.html index bd040406f..a04e2e5ce 100644 --- a/docs/reference/like.html +++ b/docs/reference/like.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/mdro.html b/docs/reference/mdro.html index 6f4a74d6a..6763dea63 100644 --- a/docs/reference/mdro.html +++ b/docs/reference/mdro.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/microorganisms.codes.html b/docs/reference/microorganisms.codes.html index 4dca81bfd..f4ef168e6 100644 --- a/docs/reference/microorganisms.codes.html +++ b/docs/reference/microorganisms.codes.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9021 + 1.2.0 diff --git a/docs/reference/microorganisms.html b/docs/reference/microorganisms.html index ffe572ef1..6ec1c4cfc 100644 --- a/docs/reference/microorganisms.html +++ b/docs/reference/microorganisms.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9021 + 1.2.0 diff --git a/docs/reference/microorganisms.old.html b/docs/reference/microorganisms.old.html index 9dbb4d48d..5ef7a925b 100644 --- a/docs/reference/microorganisms.old.html +++ b/docs/reference/microorganisms.old.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9021 + 1.2.0 diff --git a/docs/reference/mo_property.html b/docs/reference/mo_property.html index 7a23d1459..b3e0590fc 100644 --- a/docs/reference/mo_property.html +++ b/docs/reference/mo_property.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9021 + 1.2.0 diff --git a/docs/reference/mo_source.html b/docs/reference/mo_source.html index fa90545c4..d57db0173 100644 --- a/docs/reference/mo_source.html +++ b/docs/reference/mo_source.html @@ -83,7 +83,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p AMR (for R) - 1.1.0.9021 + 1.2.0 diff --git a/docs/reference/p_symbol.html b/docs/reference/p_symbol.html index 600dd4fbd..e0af51ccd 100644 --- a/docs/reference/p_symbol.html +++ b/docs/reference/p_symbol.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/pca.html b/docs/reference/pca.html index 21185ca3b..5981c2037 100644 --- a/docs/reference/pca.html +++ b/docs/reference/pca.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/proportion.html b/docs/reference/proportion.html index 73be35c88..6df56250a 100644 --- a/docs/reference/proportion.html +++ b/docs/reference/proportion.html @@ -83,7 +83,7 @@ resistance() should be used to calculate resistance, susceptibility() should be AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/resistance_predict.html b/docs/reference/resistance_predict.html index f8b4fa0bc..6385724f2 100644 --- a/docs/reference/resistance_predict.html +++ b/docs/reference/resistance_predict.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/rsi_translation.html b/docs/reference/rsi_translation.html index 0c5bf48bf..0e781a49a 100644 --- a/docs/reference/rsi_translation.html +++ b/docs/reference/rsi_translation.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0 + 1.2.0 @@ -277,7 +277,7 @@
    -

    Site built with pkgdown 1.5.0.

    +

    Site built with pkgdown 1.5.1.

    diff --git a/docs/reference/skewness.html b/docs/reference/skewness.html index 314dab683..8225249df 100644 --- a/docs/reference/skewness.html +++ b/docs/reference/skewness.html @@ -83,7 +83,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/translate.html b/docs/reference/translate.html index 64921852a..c23a5d7e2 100644 --- a/docs/reference/translate.html +++ b/docs/reference/translate.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9019 + 1.2.0